“People just really like nuns,” a theater manager of my acquaintance once said to me, explaining with a shrug the success of such sisters-infused entertainments as “The Sound of Music,” “Nunsense” and “Sister Act.” He was right, of course. We’re all fascinated by nuns. Their habits create a sense of otherness, as does the intensity and inherent selflessness of their vows. Yet sisters have also been there in the ordinary moments of many of our lives; leading, cajoling, making us feel guilty, teaching. They’re both familiar and strange, to borrow a phrase from the Russian Formalists, and thus ideal for theater and film.

American Theater Company could, then, have called its new “Catholic Repertory” — a notionally provocative and inspired pairing of John Patrick Shanley’s “Doubt” and John Pielmeier’s “Agnes of God” — the “Nun Repertory.” Not only would that probably have sold more tickets, but it actually is a pretty apt description of the common point of these two dramas, set and written about 20 years apart (“Doubt” takes place in the Bronx in 1964; “Agnes” takes place in upstate New York in 1984, although “Agnes” was actually written some two decades before “Doubt”). Both shows, which opened one after the other on Friday evening, involve earnest, hyper-intelligent Sisters in conflict with authority. Both involve horrible potential crimes which may or may have not taken place. Both are, to a large extent, about the conflict between the dictates of faith and the evidence that can dance before your eyes.

Director PJ Paparelli has pretty much blown up the old ATC space on West Byron Street (you’ll be amazed if you’ve not been here for a while) and created a much more expansive playing arena in a far more exciting theatrical environment. The new configuration was mostly in place for David Cromer’s production of “Rent,” but it’s been further developed for the Catholic Repertory, allowing the common design team, especially set designer Scott Davies and lighting designer Jesse Klug, to float both these evocative dramas in a deeply atmospheric environment that captures some of the complex majesty of the church. The stellar visual conception deftly explores a central question of both these plays: To what extent do the church’s institutions reflect the harsh realities of the world, and to what extent must they stand outside them? The director also uses the same three women — Kate Skinner, Sadieh Rifai and Penelope Walker — in all three plays, with Lance Baker, who is making quite the specialty of creepy characters like Shanley’s Father Flynn, added to the cast of “Doubt.”

So, as the nuns might say, there’s no escaping judgment for the Catholic Repertory. To put it in black-and-white terms, “Doubt” is an excellent show; “Agnes of God” doesn’t work well at all.

That’s partly a function of the two scripts. “Doubt,” which deals with a nun’s suspicion that her patriarchy is hiding an abusive priest, won the Pulitzer Prize for drama and is a masterpiece of concision. I’ve seen the piece, and the subsequent movie, two or three times before (a national tour starring the incomparable Cherry Jones played in 2007 in Chicago), but I’d forgotten, frankly, how this play never seems to waste a single word and, therefore, how much you hang on every moment. And ATC’s production is potent indeed. Skinner, who plays Sister Aloysius, is more theatrical than Jones, but very gripping; the emotionally available Rifai is a good match for Sister James, who must learn the limits of faith; and Baker offers a very carefully toned piece of acting in service of Shanley’s most important point: that those who abuse children are often so adept at hiding themselves and their actions, not only are they difficult to ferret out, their investigations might also ensnare the innocent.

You don’t see the kid in question in “Doubt,” of course, but you do see his mother. And the scene in which that African-American mom, Mrs. Muller, played here by Walker with just the right mix of determination and panic, essentially says that anyone being kind to her kid has some kind of motive is one of the most heartbreaking scenes of drama penned in the last 10 years. Paparelli’s fine production not only captures the intimacy of the piece; he also captures its magnitude. Frankly, one now views “Doubt” anew, through the prism of the Jerry Sandusky scandal. That has only made the themes of the play more powerful — and its observations about how authority figures close rank to protect themselves only seem more dangerously accurate.

“Agnes of God” deals with a novice nun (Rifai) who we know has given birth but who wants to convince a court psychologist (played by Walker) that the baby was the result of a virgin birth. The nun’s Mother Superior (Skinner) is in the middle of it all. It is still an interesting and relevant piece (and the potential consequences of childhood abuse make up one of its themes), but it’s a much woollier piece of writing than “Doubt.” Those issues are exsasperated by a much less secure production that never seems to have grabbed on to the story. Walker, who is so terrific in “Doubt,” is much less commanding in “Agnes,” wherein she does not seem totally comfortable with the text. Rifai starts out powerful, but the characterization becomes muddled with the rest of the production, and Skinner struggles, frankly, to make her second character sufficiently distinct from the first. The tension in the show dissipates just as it should be coming to a boil.

Opening two shows at once is tough. And in practice, it feels like while Paparelli’s cast his “Doubt” perfectly, that is not to so true of his “Agnes of God.” Perhaps that is a testimony to the diversity of the great Sisterhood. In earthly terms, I wouldn’t miss “Doubt,” but I’d skip “Agnes,” although you’ll have to make up your own mind about her God.